CRAN Package Check Results for Package outbreaker

Last updated on 2015-07-07 06:46:43.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1-5 3.69 26.13 29.82 ERROR
r-devel-linux-x86_64-debian-gcc 1.1-5 3.99 25.56 29.54 ERROR
r-devel-linux-x86_64-fedora-clang 1.1-5 59.20 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1-5 56.00 ERROR
r-devel-osx-x86_64-clang 1.1-5 52.83 ERROR
r-devel-windows-ix86+x86_64 1.1-5 32.00 55.00 87.00 ERROR
r-patched-linux-x86_64 1.1-5 3.96 25.47 29.42 ERROR
r-patched-solaris-sparc 1.1-5 401.20 ERROR
r-patched-solaris-x86 1.1-5 96.90 ERROR
r-release-linux-x86_64 1.1-5 4.16 27.06 31.22 ERROR
r-release-osx-x86_64-mavericks 1.1-5 OK
r-release-windows-ix86+x86_64 1.1-5 28.00 56.00 84.00 ERROR
r-oldrel-windows-ix86+x86_64 1.1-5 30.00 102.00 132.00 ERROR

Check Details

Version: 1.1-5
Check: R code for possible problems
Result: NOTE
    .kernel.expo: no visible global function definition for ‘dist’
    .kernel.expo: no visible global function definition for ‘dexp’
    .plot.kernel.expo: no visible global function definition for ‘plot’
    .plot.kernel.expo : <anonymous>: no visible global function definition
     for ‘dexp’
    as.igraph.simOutbreak : edge.col.pal: no visible global function
     definition for ‘grey’
    as.igraph.tTree : col.pal: no visible global function definition for
     ‘grey’
    disperse: no visible global function definition for ‘rnorm’
    get.Rt: no visible global function definition for ‘boxplot’
    get.Rt: no visible global function definition for ‘matplot’
    get.incid: no visible global function definition for ‘boxplot’
    get.incid: no visible global function definition for ‘matplot’
    get.tTree: no visible binding for global variable ‘median’
    outbreaker: no visible global function definition for ‘runif’
    outbreaker: no visible global function definition for ‘read.table’
    outbreaker.parallel: no visible global function definition for ‘runif’
    plot.simOutbreak: no visible global function definition for ‘plot’
    plot.tTree: no visible global function definition for ‘plot’
    plotChains: no visible global function definition for ‘matplot’
    plotChains: no visible binding for global variable ‘density’
    plotChains: no visible global function definition for ‘density’
    plotChains: no visible global function definition for ‘plot’
    plotChains : <anonymous>: no visible global function definition for
     ‘lines’
    plotOutbreak: no visible global function definition for
     ‘colorRampPalette’
    plotOutbreak: no visible global function definition for ‘boxplot’
    plotOutbreak : <anonymous>: no visible global function definition for
     ‘points’
    plotOutbreak: no visible global function definition for ‘points’
    plotOutbreak : edge.col.pal: no visible global function definition for
     ‘grey’
    plotOutbreak : drawArrow: no visible global function definition for
     ‘arrows’
    plotOutbreak : drawArrow: no visible global function definition for
     ‘text’
    selectChains: no visible global function definition for ‘anova’
    selectChains: no visible global function definition for ‘lm’
    simOutbreak : seq.dupli: no visible global function definition for
     ‘rbinom’
    simOutbreak: no visible global function definition for ‘runif’
    simOutbreak: no visible global function definition for ‘rbinom’
    simOutbreak: no visible global function definition for ‘rpois’
    transGraph : col.pal: no visible global function definition for ‘grey’
    transGraph: no visible global function definition for ‘plot’
    Undefined global functions or variables:
     anova arrows boxplot colorRampPalette density dexp dist grey lines lm
     matplot median plot points rbinom read.table rnorm rpois runif text
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 1.1-5
Check: examples
Result: ERROR
    Running examples in ‘outbreaker-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-osx-x86_64-clang, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-x86_64

Version: 1.1-5
Check: running examples for arch ‘i386’
Result: ERROR
    Running examples in 'outbreaker-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 1.1-5
Check: running examples for arch ‘x64’
Result: ERROR
    Running examples in 'outbreaker-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: simulated outbreak dataset
    > ### Title: Toy outbreak dataset used to illustrate outbreaker
    > ### Aliases: fakeOutbreak
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > ## Not run:
    > ##D ## COMMAND LINES TO GENERATE SIMILAR DATA ##
    > ##D w <- c(0, 0.5, 1, 0.75)
    > ##D ## note: this works only if outbreak has at least 30 case
    > ##D dat <- simOutbreak(R0 = 2, infec.curve = w, n.hosts = 100)[1:30]
    > ##D collecDates <- dat$onset + sample(0:3, size=30, replace=TRUE, prob=w)
    > ## End(Not run)
    >
    > ## EXAMPLE USING TOYOUTBREAK ##
    > ## LOAD DATA, SET RANDOM SEED
    > data(fakeOutbreak)
    > attach(fakeOutbreak)
    >
    > ## VISUALIZE DYNAMICS
    > matplot(dat$dynam, type="o", pch=20, lty=1,
    + main="Outbreak dynamics", xlim=c(0,28))
    > legend("topright", legend=c("S","I","R"), lty=1, col=1:3)
    >
    > ## VISUALIZE TRANSMISSION TREE
    > plot(dat, annot="dist", main="Data - transmission tree")
    > mtext(side=3, "arrow annotations are numbers of mutations")
    >
    >
    > ## Not run:
    > ##D ## RUN OUTBREAKER - PARALLEL VERSION
    > ##D ## (takes < 1 min))
    > ##D set.seed(1)
    > ##D res <- outbreaker.parallel(n.runs=4, dna=dat$dna,
    > ##D dates=collecDates,w.dens=w, n.iter=5e4)
    > ## End(Not run)
    >
    >
    > ## ASSESS CONVERGENCE OF CHAINS
    > plotChains(res)
    > plotChains(res, burnin=2e4)
    >
    > ## REPRESENT POSTERIOR ANCESTRIES
    > transGraph(res, annot="", main="Posterior ancestries", thres=.01)
    Error in layout_with_fr(list(30, TRUE, c(0, 1, 2, 3, 3, 4, 5, 5, 6, 4, :
     unused argument (rescale = FALSE)
    Calls: transGraph ... layout.fruchterman.reingold -> do_call -> eval -> eval -> layout_with_fr
    Execution halted
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64